[BioC] CDF package in R (windows)

James W. MacDonald jmacdon at med.umich.edu
Thu Jun 7 15:23:40 CEST 2007

Hi Salim,

Salim Charaniya wrote:
> Thanks a lot...
> I was able to execute the command R CMD INSTALL cdfpackage. unfortunately there is an error during execution.
> the first few steps go well (adding build stamp to DESCRIPTION, installing R files, data files, man source files,....installing help)
> (i noticed that a subdirectory named 'chm' is created in packagecdf during execution)
> The execution malfunctions at this point and i get the following error 
> hhc: not found

You should re-check your path. This indicates that you _don't_ have the 
MS HTML workshop in your path.

You could also do rcmd install --docs=txt,html,latex <packagename> which 
won't build the chm help.



> cp: cannot stat 'c://packagecdf/chm/packagecdf.chm' no such file or directory
> make[1]: ***[chm-packagecdf] Error 1
> *** Installation of packagecdf failed ***
> Acc to the manual .chm file is created by microsoft help html workshop which i have installed on the computer (and also added to the path). Any idea why i am still getting this error?
> Sorry for bothering you guys
> Thanks again
> Salim
> ----- Original Message ----
> From: Seth Falcon <sfalcon at fhcrc.org>
> To: Salim Charaniya <sal_charaniya at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Wednesday, June 6, 2007 4:35:40 PM
> Subject: Re: [BioC] CDF package in R (windows)
> Salim Charaniya <sal_charaniya at yahoo.com> writes:
>>Hi all, i am a relatively new user of bioconductor. i am using R 2.5.0
>>installed on windows. I have used bioconductor for processing affy
>>data. Last few days i have been trying to develop a CDF package for a
>>custom affy array. I downloaded the makecdfenv package and used the
>>commands in there to create a cdf package (using the .cdf file). but
>>it seems that is not enough in windows environment. I have read the
>>instructions in R installation and admin manual. Accordingly i
>>installed the windows toolset (active perl, command line tools and
>>MinGW compilers (Rtools.exe), inno setup installer). I have also
>>changed the path according to the instructions in Rtools.txt. However,
>>I cannot understand the following statement in the R manual:
>>There are a number of options available: use R CMD INSTALL
>>The same command works in Windows if you have the source-code package
>>files (option “Source Package Installation Files” in the installer)
>>and toolset (see The Windows toolset) installed.
>>I have tried this command (R cmd install path_for_cdfpackage). But it
>>is not recognized as a command and i get an error.  What are these
>>source-code package files? Where can i get them? Is there anything
>>else that i need to do to create the cdf package?
> Is the bin directory of your R also in your PATH?  Your efforts with
> makecdfenv should have produced a source package directory.  Can you
> try:
> c:\<your_path_here>\R-2.5.0\bin\R CMD INSTALL somecdfpackagedir
> I think you are close to getting things to work.
> + seth

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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